Where things live

~/.config/cydonia/       settings.toml, state.toml, mcp.toml, the agent catalogue cache
~/.local/share/cydonia/  installed agents, caches, and migration backups
<project>/.cydonia/      that project's articles, boards, tables, sessions, store and agents' worktrees

The project store

<project>/.cydonia/ holds everything written about that project, and carries a .gitignore of its own — none of it is the project's source. Copy the directory and the project's articles and boards come with it.

Agents are told to check out git worktrees under <project>/.cydonia/worktrees/, which that .gitignore keeps out of the repo.

Configuration

settings.toml is preferences: appearance, shortcuts, features, agents, the MCP server. It is written with defaults on first run, and hand-editing it is supported — see Settings.

state.toml is bookkeeping: which projects were open, where the panels were left. It answers questions only this machine can answer, so it is not worth carrying to another one.

mcp.toml holds the external MCP servers a session can reach. See MCP.

Installed agents

An agent installed from the registry is unpacked under ~/.local/share/, and its settings.toml entry points at the unpacked executable. An agent you wrote into the file yourself is never touched by the installer.

Backups

A release that changes how projects or the configuration are stored copies each file it replaces into ~/.local/share/cydonia/backup/ first. See Backups and rolling back.